Stem cells are a key element in tissue engineering and regenerative medicine. However, they require a suitable microenvironment to grow and regenerate. Carbon nanotubes (CNTs) have attracted much attention as promising materials for stem cell research due to their extraordinary properties, such as their extracellular matrix-like structure, high mechanical strength, optical properties, and high electrical conductivity. Of particular interest is the use of CNTs as biomimetic substrates to control the differentiation of stem cells. CNTs have also been combined with commonly used scaffolds to fabricate functional scaffolds to direct stem cell fate. CNTs can also be used for stem cell labeling due to their high optical absorbance in the near-infrared regime. In this paper, we review and discuss the applications of CNTs in stem cell research along with CNT toxicity issues.